If you signed the installer with a purchased certificate from a CA, you are supposed to contact the CA for explanation on why they failed to work with Microsoft to get rid of this warning.
If the certificate is not from a CA, but a self-signed certificate, you will have to resort to a CA.
Microsoft has most information published on its Windows team blog already,
https://blogs.msdn.microsoft.com/ie/2012/08/14/microsoft-smartscreen-extended-validation-ev-code-signing-certificates/
Best Practices
Developers should still follow the best practices we’ve suggested in past blog posts. We have added to that guidance the additional options of distributing apps thru the Windows Store and the option of EV code signing:
- Distribute your apps through the Windows Store
Windows 8 Applications are required to pass the Windows Store developer onboarding and application review process. Windows 8 applications are not in scope for SmartScreen application reputation checks or warnings in Windows 8.
- Digitally sign your programs (Standard or EV code signing)
Reputation is generated and assigned to digital certificates as well as specific files. Digital certificates allow data to be aggregated and assigned to a single certificate rather than many individual programs. Although not required, programs signed by an EV code signing certificate can immediately establish reputation with SmartScreen reputation services even if no prior reputation exists for that file or publisher. EV code signing certificates also have a unique identifier which makes it easier to maintain reputation across certificate renewals. Only Authenticode Certificates issued by a CA that is a member of the Windows Root Certificate Program can establish reputation.
At this time, Symantec and DigiCert are offering EV code signing certificates.
- Don’t sign or distribute malicious code
Distributing code detected as malicious will remove the reputation from a file and also any reputation from the associated digital certificate – even if signed with an EV code signing certificate.
- Apply for a Windows Logo or Windows 8 Desktop App Certification
Learn more about these programs here:
Windows 8 Desktop App Certification (required for Windows Store submissions)
Windows Logo Program